Applied Biosystems
3730 and 3730xl User Guide Rev F
User Guide
238 Pages

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Page 1
USER GUIDE
Applied Biosystems® 3730/3730xl DNA Analyzer Publication Number 4331468 Revision F
For Research Use Only. Not for use in diagnostic procedures.
The information in this guide is subject to change without notice. DISCLAIMER LIFE TECHNOLOGIES CORPORATION AND/OR ITS AFFILIATE(S) DISCLAIM ALL WARRANTIES WITH RESPECT TO THIS DOCUMENT, EXPRESSED OR IMPLIED, INCLUDING BUT NOT LIMITED TO THOSE OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, OR NON-INFRINGEMENT. TO THE EXTENT ALLOWED BY LAW, IN NO EVENT SHALL LIFE TECHNOLOGIES AND/OR ITS AFFILIATE(S) BE LIABLE, WHETHER IN CONTRACT, TORT, WARRANTY, OR UNDER ANY STATUTE OR ON ANY OTHER BASIS FOR SPECIAL, INCIDENTAL, INDIRECT, PUNITIVE, MULTIPLE OR CONSEQUENTIAL DAMAGES IN CONNECTION WITH OR ARISING FROM THIS DOCUMENT, INCLUDING BUT NOT LIMITED TO THE USE THEREOF. Limited Use Label License No. 358: Research Use Only Notice to Purchaser: The purchase of this product conveys to the purchaser the limited, non-transferable right to use the purchased amount of the product only to perform internal research for the sole benefit of the purchaser. No right to resell this product or any of its components is conveyed expressly, by implication, or by estoppel. This product is for internal research purposes only and is not for use in commercial applications of any kind, including, without limitation, quality control and commercial services such as reporting the results of purchaser's activities for a fee or other form of consideration. For information on obtaining additional rights, please contact [email protected] or Out Licensing, Life Technologies Corporation, 5791 Van Allen Way, Carlsbad, California 92008. Limited Use Label License No. 481: Sequencing or Fragment Analysis Intellectual Property Notice to Purchaser: This product is optimized for use in the DNA sequencing or fragment analysis methods covered by patents owned and/or controlled by Life Technologies Corporation ("LTC"). LTC does not convey any right or license under these patents, whether expressly, by implication, by estoppels, or otherwise, to the purchaser by the purchase of this product to use the DNA sequencing or fragment analysis methods. Notwithstanding the foregoing, a limited license to use the DNA sequencing or fragment analysis methods covered by such patents can be obtained for certain research and development activities (a) through the purchase of certain LTC reagents when such reagents are used in conjunction with an authorized LTC instrument, or (b) directly from LTC. For information on obtaining additional rights to practice the DNA sequencing or fragment analysis methods, please contact [email protected] or Out Licensing, Life Technologies Corporation, 5791 Van Allen Way, Carlsbad, California 92008. LIMITED LICENSE The Applied Biosystems® 3730 and 3730xl DNA Analyzers include patented technology licensed from Hitachi, Ltd. as part of a strategic partnership between Life Technologies and Hitachi, Ltd., as well as patented technology of Life Technologies. TRADEMARKS All trademarks are the property of Thermo Fisher Scientific and its subsidiaries unless otherwise specified. © 2014 Thermo Fisher Scientific Inc. All rights reserved.
Contents About This Guide Revision history... -vii
Chapter 1
Performing a Run Instrument Parts... 1-2 A Typical Run... 1-3 Working with Samples and Plate Assemblies... 1-5 Starting the 3730/3730xl System... 1-9 Preparing the Instrument... 1-14 Calibrating the Instrument... 1-23 Placing a Plate in the Stacker... 1-24 Running the Instrument... 1-26 Default Load Maps... 1-28 Monitoring a Run... 1-43 Working with Data in The Run History View... 1-51 Viewing Analyzed Data... 1-60
Chapter 2
3730/3730xl Data Collection Software and DNA Sequencing 3730/3730xl Data Collection Software and Sequencing Analysis Software v5.0... 2-2 About Plate Records and Sequencing... 2-4 Using the Plate Manager for Sequencing... 2-5 Working With a Results Group... 2-12 Creating an Instrument Protocol For Sequencing... 2-23 Working with Analysis Protocols for Sequencing... 2-28 Plate Search... 2-37
Chapter 3
3730/3730xl Data Collection and Fragment Analysis 3730/3730xl Data Collection Software and GeneMapper® Software Software v3.0 . . 3-2 Sample Preparation... 3-5 About Plate Records... 3-6 Using the Plate Manager For GeneMapper® Software... 3-8 Working With a Results Group... 3-13
Applied Biosystems® 3730/3730xl DNA Analyzers User Guide
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Working With Instrument Protocols For Fragment Analysis... 3-25 Using the AutoAnalysis Manager... 3-29 Plate Search... 3-35 Autoanalysis Integration... 3-39
Chapter 4
Spatial and Spectral Calibrations Spatial Calibration... 4-2 Spectral Calibration... 4-9
Chapter 5
Maintenance Instrument Maintenance... 5-2 Routine Cleaning... 5-3 Fluids and Waste... 5-9 Capillary Array... 5-12 Syringes... 5-18 Polymer Blocks... 5-21 Checking Available Space on Drives D, E, and F... 5-30 Hard Disk Status... 5-31 Deleting Records from the Database... 5-32
Appendix A Error Messages Error Messages... A-2
Support Obtain SDSs... Support-1 Obtain support... Support-1 Limited Product Warranty... Support-1
Safety Symbols on Instruments...
Safety-2
Safety Labels on Instruments... Safety-4 General Instrument Safety... Safety-6 Chemical Safety... Safety-6 Chemical Waste Safety... Safety-7 Electrical Safety... Safety-8 Physical Hazard Safety... Safety-8 Biological Hazard Safety... Safety-9 iv
Applied Biosystems® 3730/3730xl DNA Analyzers User Guide
Laser Safety... Safety-10 Bar Code Scanner Laser Safety... Safety-11 Computer Workstation Safety... Safety-11 Safety and Electromagnetic Compatibility (EMC) Standards... Safety-11
Index
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Applied Biosystems® 3730/3730xl DNA Analyzers User Guide
About This Guide
IMPORTANT! Before using this product, read and understand the information the “Safety” section in this document.
Revision history Revision F
Date September 2014
Applied Biosystems® 3730/3730xl DNA Analyzers Getting User Guide
Description Update laser information in Safety section.
vii
About This Guide
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Applied Biosystems® 3730/3730xl DNA Anayzers User Guide
Performing a Run In This Chapter
1
1
Instrument Parts... 1-2 A Typical Run... 1-3 Working with Samples and Plate Assemblies... 1-5 Starting the 3730/3730xl System... 1-9 Preparing the Instrument... 1-14 Calibrating the Instrument... 1-23 Placing a Plate in the Stacker... 1-24 Running the Instrument... 1-26 Default Load Maps... 1-28 Monitoring a Run... 1-43 Working with Data in The Run History View... 1-51 Viewing Analyzed Data... 1-60
Applied Biosystems® 3730/3730xl DNA Analyzers User Guide
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Chapter 1 Performing a Run
Instrument Parts Oven door
Stacker door Polymer syringe Anode buffer jar
Upper polymer block Lower polymer block Interior light button
Stacker door indicator light Waste reservoir
Polymer reservoir
Water reservoir
Power button (on/off)
Instrument Status Lights
Figure 1-1
1-2
Buffer reservoir (position) Tray button (unloads current tray from the capillary array
GR2140
Parts of the 3730/3730xl DNA Analyzers
Applied Biosystems 3730/3730xl DNA Analyzers User Guide
A Typical Run
A Typical Run Flowchart of a Typical Run
This flowchart provides an overview of the steps required to perform a run on the 3730/3730xl DNA Analyzers. Turn on the computer Turn on the instrument; wait for solid green light Launch 3730/3730xl Data Collection software Set up the instrument: ¥ Prepare the syringe ¥ Install the polymer blocks ¥ Install the capillary array ¥ Add or change the polymer ¥ Fill the reservoirs ¥ Place the reservoirs onto the deck Yes
Spatial calibration done?
No Perform calibration
Don't know
Yes
Spectral calibration done?
Display and check calibration
No Create instrument protocol Prepare plate record Place plate in the stacker Perform calibration
Don't know
Display and check calibration
Continued on next page Figure 1-2
GR2200b
¥ Create an Instrument Protocol ¥ Create Analysis Protocol ¥ Create a Results Group
Typical Run Flowchart, Part I
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Chapter 1 Performing a Run
Continued from previous page Spectral calibration, Protocols, and Results Group done
OR
Manual mode
Auto mode
Create Plate Record in Plate Manager
Import/Create Plate Record in Plate Manager
Link plate to Plate Record, using external barcode reader
(Optional) Link plate to Plate Record, using external barcode reader
Prepare samples and plate assemblies
Prepare samples and plate assemblies
Schedule plates in the Run Scheduler
Place plates in the stacker
View and archive data
Figure 1-3
1-4
GR2200b
Start and monitor run
Typical Run Flowchart, Part II
Applied Biosystems 3730/3730xl DNA Analyzers User Guide
Working with Samples and Plate Assemblies
Working with Samples and Plate Assemblies Preparing Samples References for Sample Preparation
For information on required materials, sample preparation, and plate centrifugation, see: • Sequencing: Applied Biosystems® 3730/3730xl DNA Analyzer Chemistry Guide (P/N 4331467).
• Fragment analysis: See this guide, page 3-5.
Checking the Plate
After centrifuging the plate of samples, ensure each sample is positioned at the bottom of its tube or well. To check the plate of samples:
1. Hold the plate up to a light source. Your samples should: Look like this...
Not look like this...
Not look like this...
The sample is positioned correctly in the bottom of the well.
The sample lies on the side wall because the plate was not centrifuged.
An air bubble lies at the bottom of the well because the plate was not: • Centrifuged with enough force, or • Centrifuged for enough time
2. If any sample is not positioned at the bottom of the well, recentrifuge the plate.
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Chapter 1 Performing a Run
Working with Plate Assemblies Overview
You have two options to prevent sample evaporation: • Use septa with a plate • Use a heat-sealed film with a plate.
Only use a gray base with a heat-sealed film and only use a black base with septa.
96-well Plate Assembly Using Septa
Plate retainer
Notched corners Plate septa
GR2194
Sample plate
Black plate base
Figure 1-4
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Septa Based Plate Assembly
Applied Biosystems 3730/3730xl DNA Analyzers User Guide
Working with Samples and Plate Assemblies
384-well Plate Assembly Using a Heat-sealed Plate
Plate retainer
Heat seal film
GR2196
Heat-sealed sample plate
Gray plate base
Heat Sealed Film Based Plate Assembly
Figure 1-6
Assembled plate components
GR2199
Figure 1-5
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Chapter 1 Performing a Run
Preparing a Plate Assembly Using Septa
To prepare a plate assembly using a septum:
1. Secure a clean and dry plate septum on the sample plate. IMPORTANT!
• Never use warped plates. • Ensure the plate septum lies flat on the plate. • Ensure that the plate retainer and the septum holes are aligned. Damage to the array tips may occur if they are not aligned (see figure 1-7 below). • Do not denature plate with septa in place. 2. Place the sample plate into the plate base. 3. Snap the plate retainer onto the plate and then into the black plate base. 4. Ensure the plate retainer holes are aligned with the holes in the septum strip.
Figure 1-7
Preparing a Plate Assembly Using a Heat-sealed Plate
Align the plate sample holes with the septum holes.
The following equipment is needed to heat-seal plates: • Thermal plate sealer • 3-mil thick plastic heat seal film (P/N 4337570). The film is 1-mil thick after heating.
Do not use metallized heat seal film. They may damage the instrument’s piercing needles.
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Applied Biosystems 3730/3730xl DNA Analyzers User Guide
Starting the 3730/3730xl System
Starting the 3730/3730xl System About Naming the Computer
Do not rename the computer once 3730/3730xl DNA Analyzer Data Collection Software has been installed. Doing so may cause the 3730/3730xl Data Collection software to malfunction.
Starting the Computer Starting the Computer Workstation
IMPORTANT! Start the computer workstation before starting the 3730/3730xl DNA
Analyzers. To start the computer workstation:
1. Turn on the monitor. 2. Power on the computer. The computer boots and then the Begin Logon dialog box displays. 3. Enter the user name and password. • The default user name for the workstation is 3730User. Do not change this user name. • There is no default password. If you would like to use a password, your system administrator can create one. • If the computer is connected to a network, you do not need to log on to the network before starting the instrument.
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Chapter 1 Performing a Run
Starting the Instrument Starting the Instrument
To start the 3730/3730xl DNA Analyzer:
1. On the instrument, ensure that the: • Oven door is closed • Instrument door is closed • Stacker drawer is closed • Buffer, water, and waste trays are loaded 2. On the computer, ensure that the: • Computer is powered on (see “Starting the Computer” on page 1-9) • Microsoft® Windows® 2000 operating system has loaded IMPORTANT! The computer must be on and running the Windows 2000 operating system before starting the instrument because the instrument must copy the firmware from the computer.
3. Turn on the instrument by pressing the on/off power button on the front of the instrument. Ensure the green status light is on and constant before proceeding (this takes about 1 minute). • While the instrument is booting up and performing self-checks, the yellow status light flashes. • If a solid green light does not display, launch the 3730/3730xl software and look at the event log messages (see page 1-47). The event log messages are located at: E:AppliedBiosystemsUDCData CollectionDataga3730Instrument Name Note: If the instrument door is open during power-on, the yellow light flashes
indicating that the boot-up has not completed. Close the instrument door and wait until the solid green status light displays (this takes 15-20 seconds).
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Applied Biosystems 3730/3730xl DNA Analyzers User Guide
Starting the 3730/3730xl System
Starting the 3730/3730xl Data Collection Software
To start the 3730/3730xl Data Collection software:
1. Select Start > Programs > AppliedBiosystems > Unified Data Collection > Run Unified Data Collection v1.0 software.
The Service Console displays. By default, all applications are off as indicated by the red circles. However, they launch automatically with the 3730/3730xl Data Collection software.
Figure 1-8
Service Console with all applications off
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Chapter 1 Performing a Run
As each application automatically activates, the red circles (off) change to yellow triangles (activating), to green squares (on) when they are fully functional.
On
Activating Off
Figure 1-9
Service Console with applications activating
Figure 1-10
Service Console with all applications on Right-click an object (circle, square, or triangle) to display a menu: a. Click Start to start an application. Start is disabled if the application is already running. b. Click Stop to stop an application. Stop is disabled if the application is already stopped or just starting. Note: Click Show Console to display the Console Viewer window
IMPORTANT! If you use the right-click method to manually start the applications, they must be started in order from top to bottom, and you must wait until an application is running (green square) before starting the application below it.
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Applied Biosystems 3730/3730xl DNA Analyzers User Guide